TB-Profiler result

Run: SRR7796667
Summary

Run ID: SRR7796667

Sample name:

Date: 04-04-2023 20:20:46

Number of reads: 564863

Percentage reads mapped: 70.65

Strain: lineage2.2.2

Drug-resistance: Pre-XDR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.99
lineage2.2.2 East-Asian (Beijing) Beijing-RD105/RD207 RD105;RD207 0.99
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs
gyrA 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 0.96 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289214 p.Gln10* stop_gained 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4326110 p.Trp455* stop_gained 0.13 ethionamide
ethA 4326130 c.1343delA frameshift_variant 1.0 ethionamide, ethionamide
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction
gyrB 7173 p.Asp645Val missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 760111 p.Ser102Phe missense_variant 0.15
rpoC 762632 c.-738C>T upstream_gene_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764616 p.Asn416Ser missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 778743 p.Val55Met missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781406 c.-154_-153insC upstream_gene_variant 1.0
rpsL 781868 c.309T>C synonymous_variant 0.1
rpsL 781871 c.312G>C synonymous_variant 0.11
Rv1258c 1406377 p.Gly322Ser missense_variant 0.14
embR 1416693 p.Asp219Asn missense_variant 0.14
atpE 1461282 p.Val80Ile missense_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473492 n.-166T>C upstream_gene_variant 0.11
rrl 1474887 n.1230T>C non_coding_transcript_exon_variant 0.12
rrl 1475578 n.1921C>T non_coding_transcript_exon_variant 1.0
inhA 1673406 c.-796C>T upstream_gene_variant 1.0
rpsA 1833909 p.Asp123Ala missense_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834927 c.1386A>G synonymous_variant 0.1
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918485 c.546G>A synonymous_variant 0.12
katG 2154014 p.Ser700Thr missense_variant 0.1
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155068 c.1044T>A synonymous_variant 0.2
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168801 c.1812A>G synonymous_variant 0.11
PPE35 2169202 p.Ser471Pro missense_variant 0.11
PPE35 2170024 p.Thr197Ser missense_variant 0.2
Rv1979c 2223195 c.-32delT upstream_gene_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290079 c.-838T>A upstream_gene_variant 0.11
kasA 2517975 c.-140A>T upstream_gene_variant 0.1
ahpC 2726245 p.Leu18His missense_variant 0.11
ahpC 2726684 c.492G>A synonymous_variant 0.11
ribD 2986828 c.-11C>T upstream_gene_variant 0.11
thyA 3073867 p.Thr202Ile missense_variant 0.1
thyA 3074122 p.Asp117Gly missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474225 c.219C>T synonymous_variant 0.2
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
clpC1 4038364 p.Ile781Phe missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4246085 p.Glu951Asp missense_variant 0.13
embB 4246583 p.Arg24Cys missense_variant 0.4
aftB 4267203 p.Lys545Arg missense_variant 0.11
aftB 4267419 p.Ala473Val missense_variant 0.11
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268394 p.Leu148Pro missense_variant 0.14
ubiA 4269784 p.Val17Glu missense_variant 0.1
ubiA 4269911 c.-78G>A upstream_gene_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0